Defining the struggle
The central conflict in the world today is the massive struggle -- often and accurately called a "culture war" -- between secular modernity and what I call "malignant traditionalism", which consists mostly of militant religion, especially Christianity and Islam. These religions' historical impact and continuing influence are, I believe, so destructive and dangerous that in the long run our goal must be to eradicate them from our societies.
How feasible that is, and in what time-frame, is a whole complex issue in itself. My concern here is the risk of the goal being misunderstood by people unfamiliar with atheist thinking. Religionists like to respond to our every success at getting their boot off our necks by screaming that we are "persecuting" them. The claim has no credibility, not just because we aren't persecuting them, but because doing so would not serve our real purposes.
A religion is not a group of people. It's a set of beliefs of the type Richard Dawkins calls "memes", which has in a very real sense "evolved" to take root and spread in its available environment, which is human minds. I consider a religion a sort of mental parasite which uses humans as host organisms and modifies their behavior with the goal of spreading the religion to others, as parasites in the natural world do.
It's a distinction, however, that not everyone grasps, as can be seen from the comment thread here. The linked post focuses on the recent decree by the Saudi Arabian regime declaring advocacy of atheism, or any kind of opposition to the regime, to be "terrorism". An act characteristic of a tyrannical theocracy, but the comment thread itself is dominated by a hysterical and incoherent individual declaring all Muslims to be irredeemably slaves to their religion and calling on them to be "nuked" -- read it for yourself, I'm using sanitized language here. I actually doubt that this person is an atheist, since one almost never sees atheists using such violent rhetoric, but the point remains.
You can see my responses at the link. The point I want to emphasize here is that in the war against religion, most religious people are not the enemy -- they are the battlefield. Yes, some (mostly leaders, such as Khomeini or Ratzinger) are genuinely evil and have to be treated as such -- but in most cases we're dealing with, not an army, but a population afflicted with an epidemic. This is a "war" more like the war on, say, AIDS or malaria than like a literal war.
We've been fighting it this way for centuries, and achieved a great deal thereby. Compared with the situation 400 years ago when religion was all-powerful, the Western world has already traveled 90% of the way to a religion-free society. That was not accomplished by force or violence (even though the enemy has often used violence against us). It was achieved by using a wide variety of persuasive techniques (including, as I've stressed elsewhere, ridicule) to undermine the parasite's grip on the minds under its dominion, eventually uprooting it or, more commonly, weakening its effects to a nearly negligible level, reducing religion to a mere label devoid of fervor. With the recent rise of "New Atheism" and its far more aggressive lines of attack, unbelief has proliferated in the United States with astonishing speed, while the Christian Right shrinks and loses ground even while growing more extremist and militant. A large minority of Americans are now non-religious, while far more adhere to a Christianity so shallow and vapid that it no longer presents a substantial threat. These persuasive techniques are the only weapons we need. They are working.
They are working even in places that seem utterly unpromising. Iranian atheist blogger Kaveh Mousavi explains here how he has had great success at bringing fellow Iranians around to discard Islam and embrace atheism, by showing them how the mushy "moderate" position is untenable. That's the way to get this done -- the Middle East will be de-Islamized the same way the West is being de-Christianized, and Middle Eastern atheists are in the best position to lead the process. Crazed rhetoric about throwing nuclear bombs around, or violence more generally, is not just useless -- it's offensively stupid.
Eradicating religion does not mean killing or persecuting religious people any more than eradicating AIDS means killing or persecuting AIDS patients, and for the same reason.